Long story short, one of my trolling motor battery shows negative when on volt meter, and 3.6 reversed.
New to me so took to Autozone. Guy says to drain completely then recharge.
Not sure how it happened. My questions are how do I then charge it positive to positive?
Then how do I hook it back in my system? It's on a 36v trolling motor
Thanks for any knowledgeable replies.

The long story short not mentioned part surely is that you at some point ran most all the trolling motors batteries fully dead causing the reverse polarity on one.

Have permanently affected the batteries and they will have reduced lives if they are recoverable at all.

You might attempt recharge as regular....neg to neg, pos to pos. The battery cannot survive for long being used as reverse charged. A small 12 volt incandescent auto bulb can pull the reverse charge off.

An automotive style charger may be needed to get some initial charge in each to a point where your regular charger will pick up and finish chargeing.

In future, monitor the voltage of each battery occasionally to make sure no battery will dip below 50% state of charge... about 12. 2 volts. Even the weakest battery in the series cannot be polarity reversed if you check the voltages and stop trolling to recharge when needed. It that is too soon, replace the weakest battery or all if they are all getting over-discharged).

Thanks